It is the third time in as many matches that disturbances have been reported at the London Stadium, the former Olympic Stadium and the Hammers’ home since last month.
An FA spokesperson said: “We have been in touch with the club and the relevant authorities and there will be more conversations on Monday.”
West Ham say they “unreservedly condemn” the behaviour of some spectators at Saturday’s fixture, in which Watford came from two goals behind to win 4-2, and would pursue bans for those involved.
“While these isolated incidents were quickly brought under control, this behaviour has no place in football and West Ham United will work tirelessly to eradicate such incidents,” the club said.
“Our policy on this behaviour remains one of zero tolerance and we will work with the police and other stakeholders to identify the individuals involved. Once identified, they will be banned from attending any West Ham United fixture for life and we will request the courts serve banning orders to prevent these individuals attending any football.”
Clashes between rivals fans were reported at West Ham’s first league game at their new home, against Bournemouth last month, while some supporters were filmed fighting in the ground as the club crashed out of the Europa League against Romanian side Astra Giurgiu days later.
West Ham, who pay £2.5m per year to use the ground on match days only, said the stadium’s operators were responsible for hiring and managing stewards and security at the 56,000-seater venue.
We are trying to achieve harmony between fans who want to sit and those who what to stand and increase to 66k. dg https://t.co/Zd1dlh4nvn— David Gold (@davidgold) September 10, 2016
Hammers co-chairman David Gold has vowed to resolve the issue of some supporters standing during games, which is believed to have caused friction.
He said: “We are trying to achieve harmony between those who want to sit and those who want to stand.”